Zinc in PDB 5kl2: Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna

The structure of Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna, PDB code: 5kl2 was solved by H.Hashimoto, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.12 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.107, 65.089, 35.702, 90.00, 93.42, 90.00
R / Rfree (%)	16.4 / 19.3

The structure of Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna (pdb code 5kl2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna, PDB code: 5kl2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:20.6 occ:1.00 NE2 A:HIS377 2.0 22.7 1.0 NE2 A:HIS373 2.1 19.9 1.0 SG A:CYS355 2.3 22.1 1.0 SG A:CYS360 2.3 23.3 1.0 CD2 A:HIS377 3.0 20.6 1.0 CD2 A:HIS373 3.0 16.2 1.0 CE1 A:HIS377 3.0 23.6 1.0 HB3 A:CYS355 3.0 30.5 1.0 CB A:CYS355 3.1 25.4 1.0 HB3 A:CYS360 3.1 26.9 1.0 CE1 A:HIS373 3.1 21.5 1.0 CB A:CYS360 3.1 22.4 1.0 HD2 A:HIS377 3.1 24.7 1.0 HD2 A:HIS373 3.1 19.4 1.0 HB2 A:CYS360 3.2 26.9 1.0 HE1 A:HIS377 3.2 28.3 1.0 HB2 A:CYS355 3.3 30.5 1.0 HE1 A:HIS373 3.3 25.8 1.0 HB2 A:PHE357 3.5 29.3 1.0 HB2 A:ARG362 3.7 43.0 1.0 ND1 A:HIS377 4.1 26.4 1.0 CG A:HIS377 4.1 25.2 1.0 CG A:HIS373 4.2 16.1 1.0 ND1 A:HIS373 4.2 16.3 1.0 HG2 A:GLN374 4.4 29.6 1.0 H A:ARG362 4.4 28.2 1.0 H A:PHE357 4.4 31.8 1.0 CB A:PHE357 4.4 24.4 1.0 HD1 A:PHE357 4.5 27.0 1.0 CA A:CYS355 4.5 24.6 1.0 CA A:CYS360 4.6 21.8 1.0 CB A:ARG362 4.6 35.9 1.0 HG3 A:ARG362 4.6 42.7 1.0 HA A:GLN374 4.7 24.4 1.0 HB3 A:PHE357 4.8 29.3 1.0 HA A:CYS360 4.8 26.2 1.0 HA A:CYS355 4.9 29.6 1.0 HD1 A:HIS377 4.9 31.7 1.0 CD1 A:PHE357 4.9 22.5 1.0 HE21 A:GLN374 4.9 37.2 1.0 C A:CYS355 5.0 24.4 1.0 HB3 A:ARG362 5.0 43.0 1.0 HD1 A:HIS373 5.0 19.6 1.0 CG A:PHE357 5.0 24.4 1.0

Zinc binding site 2 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:24.4 occ:1.00 NE2 A:HIS401 2.1 19.0 1.0 NE2 A:HIS405 2.1 27.0 1.0 SG A:CYS388 2.3 26.5 1.0 SG A:CYS385 2.3 24.1 1.0 CD2 A:HIS405 2.9 26.6 1.0 HD2 A:HIS405 2.9 32.0 1.0 CE1 A:HIS401 3.0 23.1 1.0 CD2 A:HIS401 3.1 19.2 1.0 H A:CYS388 3.1 33.8 1.0 HB3 A:CYS385 3.1 29.7 1.0 HB3 A:CYS388 3.2 36.5 1.0 CB A:CYS385 3.2 24.7 1.0 HE1 A:HIS401 3.2 27.8 1.0 CE1 A:HIS405 3.2 31.9 1.0 HD2 A:HIS401 3.3 23.1 1.0 CB A:CYS388 3.3 30.4 1.0 HB2 A:CYS385 3.3 29.7 1.0 HB A:THR387 3.5 31.6 1.0 HE1 A:HIS405 3.5 38.2 1.0 N A:CYS388 3.7 28.1 1.0 CA A:CYS388 4.0 29.5 1.0 HB3 A:ARG390 4.1 35.3 1.0 CG A:HIS405 4.1 27.1 1.0 HB2 A:CYS388 4.1 36.5 1.0 ND1 A:HIS401 4.2 17.7 1.0 CG A:HIS401 4.2 15.8 1.0 ND1 A:HIS405 4.2 28.8 1.0 H A:ARG390 4.3 32.9 1.0 H A:THR387 4.3 34.5 1.0 CB A:THR387 4.4 26.4 1.0 HG22 A:THR387 4.6 35.0 1.0 H A:GLN389 4.6 36.8 1.0 C A:THR387 4.6 34.6 1.0 CA A:CYS385 4.7 21.3 1.0 C A:CYS388 4.7 28.6 1.0 HB2 A:ARG390 4.7 35.3 1.0 HG1 A:THR404 4.7 29.7 1.0 HA A:THR402 4.8 19.4 1.0 HE2 A:PHE392 4.8 40.0 1.0 HA A:CYS388 4.9 35.4 1.0 CB A:ARG390 4.9 29.4 1.0 CA A:THR387 4.9 34.0 1.0 CG2 A:THR387 4.9 29.1 1.0 N A:GLN389 4.9 30.6 1.0 N A:THR387 4.9 28.7 1.0 HD1 A:HIS401 4.9 21.2 1.0 HG21 A:THR387 5.0 35.0 1.0

Zinc binding site 3 out of 3 in the Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Wilms Tumor Protein (WT1) ZNF2-4 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:26.1 occ:1.00 NE2 A:HIS435 2.0 36.4 1.0 NE2 A:HIS431 2.0 21.0 1.0 SG A:CYS413 2.3 24.9 1.0 SG A:CYS418 2.3 30.6 1.0 CE1 A:HIS435 2.9 35.2 1.0 CD2 A:HIS431 2.9 23.6 1.0 HB3 A:CYS418 3.0 34.4 1.0 HE1 A:HIS435 3.0 42.2 1.0 CD2 A:HIS435 3.0 35.4 1.0 HD2 A:HIS431 3.0 28.3 1.0 CE1 A:HIS431 3.1 27.6 1.0 HB2 A:CYS413 3.1 27.8 1.0 CB A:CYS418 3.1 28.7 1.0 CB A:CYS413 3.2 23.1 1.0 HD2 A:HIS435 3.3 42.5 1.0 HB2 A:CYS418 3.3 34.4 1.0 HE1 A:HIS431 3.3 33.1 1.0 HB3 A:CYS413 3.3 27.8 1.0 HB2 A:TRP415 3.5 38.9 1.0 HD2 A:LYS420 3.6 76.2 1.0 HB2 A:LYS420 3.6 34.6 1.0 ND1 A:HIS435 4.0 38.8 1.0 CG A:HIS431 4.1 22.3 1.0 CG A:HIS435 4.1 33.0 1.0 ND1 A:HIS431 4.1 24.1 1.0 H A:LYS420 4.3 31.7 1.0 HD1 A:TRP415 4.4 62.1 1.0 CB A:TRP415 4.4 32.4 1.0 H A:TRP415 4.4 32.9 1.0 CD A:LYS420 4.5 63.5 1.0 HD2 A:HIS432 4.5 45.3 1.0 CA A:CYS418 4.6 30.4 1.0 CB A:LYS420 4.6 28.8 1.0 CA A:CYS413 4.6 21.6 1.0 HB3 A:TRP415 4.7 38.9 1.0 HD1 A:HIS435 4.8 46.6 1.0 HD3 A:LYS420 4.8 76.2 1.0 HA A:CYS413 4.8 25.9 1.0 HE1 A:MET434 4.9 77.8 1.0 HA A:CYS418 4.9 36.5 1.0 CD1 A:TRP415 4.9 51.8 1.0 HD1 A:HIS431 4.9 28.9 1.0 C A:CYS418 4.9 36.9 1.0 HE2 A:PHE422 5.0 31.6 1.0 HZ2 A:LYS420 5.0 0.7 1.0 CG A:TRP415 5.0 51.7 1.0

H.Hashimoto, X.Zhang, Y.Zheng, G.G.Wilson, X.Cheng. Denys-Drash Syndrome Associated WT1 Glutamine 369 Mutants Have Altered Sequence-Preferences and Altered Responses to Epigenetic Modifications. Nucleic Acids Res. V. 44 10165 2016.
ISSN: ESSN 1362-4962
PubMed: 27596598
DOI: 10.1093/NAR/GKW766